15-30802276-A-G

Variant names:

• chr15-30802276-A-G
• rs12438793
• XM_017022809.1:c.*114A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XM_017022809.1(LOC101930434):​c.*114A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0821 in 152,324 control chromosomes in the GnomAD database, including 600 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.082 (600 hom., cov: 32)
• Consequence: LOC101930434 XM_017022809.1 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.187
• Publications: 3 publications found

Genes affected

LOC101930434 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.122 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101930434	XM_017022809.1	c.*114A>G		3_prime_UTR_variant	Exon 8 of 8		XP_016878298.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000307338	ENST00000825164.1	n.47+791A>G		intron_variant	Intron 1 of 6

Frequencies

GnomAD3 genomes AF: 0.0820 AC: 12488 AN: 152206 Hom.: 600 Cov.: 32

Gnomad AFR AF: 0.0484

Gnomad AMI AF: 0.0932

Gnomad AMR AF: 0.126

Gnomad ASJ AF: 0.127

Gnomad EAS AF: 0.108

Gnomad SAS AF: 0.0993

Gnomad FIN AF: 0.0450

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.0924

Gnomad OTH AF: 0.0931

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0821 AC: 12511 AN: 152324 Hom.: 600 Cov.: 32 AF XY: 0.0810 AC XY: 6034 AN XY: 74476

African (AFR) AF: 0.0487 AC: 2025 AN: 41578

American (AMR) AF: 0.126 AC: 1934 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.127 AC: 439 AN: 3468

East Asian (EAS) AF: 0.108 AC: 558 AN: 5184

South Asian (SAS) AF: 0.0994 AC: 480 AN: 4830

European-Finnish (FIN) AF: 0.0450 AC: 478 AN: 10614

Middle Eastern (MID) AF: 0.112 AC: 33 AN: 294

European-Non Finnish (NFE) AF: 0.0924 AC: 6284 AN: 68030

Other (OTH) AF: 0.0922 AC: 195 AN: 2116

Alfa AF: 0.0891 Hom.: 815

Bravo AF: 0.0855

Asia WGS AF: 0.110 AC: 382 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	2.9
DANN	Benign	0.52
PhyloP100		0.19

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs12438793; hg19: chr15-31094479;